RetrogeneDB ID: retro_pabe_156

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:123948708..123949536(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000016975
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000008259
• Aliases: None
• Description: Cytochrome c oxidase assembly protein COX11, mitochondrial [Source:UniProtKB/TrEMBL;Acc:H2NTL1]

Sequence

>retro_pabe_156
ATGGGAGGACTCTGGCGTCCGGGATGGAGGCGCGTAGCTTTCTGTGGCTGGCGCTGGATCCACCCTGGGTCTCCAACTAG
GGCTGCAGAGAGGGTAGAGCCGTTTCTTAGGCCAGAGTGCAGTGGGACAGGAGGTGCCGGGAGAGGACTGAGGTGGCTTG
GGACATGGAAGCGCTGCAGCCTTCGAGCCCGGCATCCAGCATTGCAGCCGCCGCGGCGGCATAAGAGCTCGAACCCTTTC
ACACGCGCGCAGAAGGAGGAGTGGCGGCGGCGGAACAAGACGACCCTAACTTACGTGGCCGCTGTCGCCGTGGGCATGCT
TGGGGCGTCCTACGCTGCCGTACCCCTTTATCGGCTCTATTGCCAGACTACTGGACTTGGAGGATCAGCCCTTGCAGGTC
ATGCCTCAGACAAGATTGAAAACATGGTGCCTGTTAAAGATCGAATCATTAAAATTAGCTTTAATGCAGATGTGCATGCA
AGTCTCCAGTGGAACTTTAGACCTCAGCAAACAGAAATATATGTGGTGCCAGGAGAGACTGCACTGGCATTTTACAGAGC
TAAGAATCCTACTGACAAACCAGTAATTGGAATTTCTACATACAATATTGTTCCATTTGAAGCTGGACAGTATTTCAATA
AAATACAGTGCTTCTGTTTTGAAGAACAAAGGCTTAATCCCCAAGAGGAAGTAGATATGCCAGGGTTTTTCTACATTGAT
CCTGAATTTGCTGAAGATCCAAGAATGATTAAAGTTGATCTTATCACTCTTTCTTACACTTTTTTTGAAGCAAAGGAAGG
GCACAAGTTGCCAGTTCCAGGATATAAT

Alignment

ORF - retro_pabe_156 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.55 %
• Parental protein coverage: 96.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGGLWRPGWRRVAFCGWRWIHPGSPTRAAERVEPFLRPECSGTGGAGRGLRWLGTWKRCSLGARHPALQP
          MGGLWRPGWRRVAFCGWRWIHPGSPTRAAERVEPFLRPECSGTGGAGRGLRWLGTWKRCSL.ARHPALQP
Retrocopy MGGLWRPGWRRVAFCGWRWIHPGSPTRAAERVEPFLRPECSGTGGAGRGLRWLGTWKRCSLRARHPALQP

Parental  PRRHKNSNPFTRAQKEEWRRRNKTTLTYVAAVAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGHASDKIE
          PRRHK.SNPFTRAQKEEWRRRNKTTLTYVAAVAVGMLGASYAAVPLYRLYCQTTGLGGSA.AGHASDKIE
Retrocopy PRRHKSSNPFTRAQKEEWRRRNKTTLTYVAAVAVGMLGASYAAVPLYRLYCQTTGLGGSALAGHASDKIE

Parental  NMVPVKDRIIKISFNADVHASLQWNFRPQQTEIYVVPGETALAFYRAKNPTDKPVIGISTYNIVPFEAGQ
          NMVPVKDRIIKISFNADVHASLQWNFRPQQTEIYVVPGETALAFYRAKNPTDKPVIGISTYNIVPFEAGQ
Retrocopy NMVPVKDRIIKISFNADVHASLQWNFRPQQTEIYVVPGETALAFYRAKNPTDKPVIGISTYNIVPFEAGQ

Parental  YFNKIQCFCFEEQRLNPQEEVDMPVFFYIDPEFAEDPRMIKVDLITLSYTFFEAKEGHKLPVPGYN
          YFNKIQCFCFEEQRLNPQEEVDMP.FFYIDPEFAEDPRMIKVDLITLSYTFFEAKEGHKLPVPGYN
Retrocopy YFNKIQCFCFEEQRLNPQEEVDMPGFFYIDPEFAEDPRMIKVDLITLSYTFFEAKEGHKLPVPGYN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.94 RPM	5.81 RPM
SRP007412_cerebellum	0.24 RPM	8.63 RPM
SRP007412_heart	0.66 RPM	6.05 RPM
SRP007412_kidney	0.63 RPM	20.12 RPM
SRP007412_liver	0.09 RPM	12.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_156 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_156 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008482	1 retrocopy	retro_cpor_1340,
Dasypus novemcinctus	ENSDNOG00000014862	1 retrocopy	retro_dnov_1933,
Dipodomys ordii	ENSDORG00000001207	1 retrocopy	retro_dord_180,
Homo sapiens	ENSG00000166260	1 retrocopy	retro_hsap_3442,
Microcebus murinus	ENSMICG00000005225	1 retrocopy	retro_mmur_1119,
Monodelphis domestica	ENSMODG00000014855	1 retrocopy	retro_mdom_952,
Mus musculus	ENSMUSG00000020544	4 retrocopies	retro_mmus_1318, retro_mmus_2318, retro_mmus_2714, retro_mmus_986,
Nomascus leucogenys	ENSNLEG00000007990	1 retrocopy	retro_nleu_2297,
Ochotona princeps	ENSOPRG00000004138	1 retrocopy	retro_opri_441,
Pongo abelii	ENSPPYG00000008259	2 retrocopies	retro_pabe_156 , retro_pabe_2847,
Pan troglodytes	ENSPTRG00000009422	1 retrocopy	retro_ptro_2335,
Rattus norvegicus	ENSRNOG00000046318	1 retrocopy	retro_rnor_1515,